Sequence
atgc intronic sequence ATGC exonic sequencegtttcttagctccatttgttggtcattgacatgtaatattcttttgacagatggtcatgttgtttacagtgaggttattattctgattttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA
Basic information
species | Glycine max |
transcript | GLYMA01G42140.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g18030.1 (Oryza sativa), 3'ss of exon 10
-----------------------------gtttcttagctc-catttgttggtcattgacatgtaatattct--tttgacagatggtcatgttgtttacagtgagg--ttattattctgatt---------ttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA
||||| | | |||| | | || | || | |||||| || || ||| | || | | || || | || || || |||| || || | || || |||||||| ||||||||||||||||||||| | || ||||| || || || ||||| || |
gtatgaggtggaatgtcaaacttcaagtcatttctggggtgatttttgcaattttcccttttttagtgttttagtttgactgactaccacattgaatgaagcaatgatttgttctcatgtttccttaatgttttcagATCGCACCAATTATTCACGAATGGACCTATGATGCCATGTGTCATGATCTACTCTGCATGGATGGCAACAAGTATGTACAACAG
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 9
--gtttcttagctccatttgttggtcattgacatgtaatattct---tttgacagatggtcatgttgtttaca-gtgaggttattattctgattttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA
| | || || ||| | | | | | |||| || | ||||| | | ||| | || || | || | | ||||||| || | || |||||||||||||||||||| |||||||||||| |||| |||||| || || || |||||||||||
gtatatgttgaacatatatgtgatttaaccattatttttcttctacattgagtaaatggtgttaatctttttataccgctttgtttctttggtacttcagATTGCACCAATTATTCATGAATGGACTTATGATGCTATGTGTCATGATCTGCTTTGTATGGATGGCAACAAGTATGTTCATGAG
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 9
gtttcttagctccatttgttggtcattgacatgtaatattcttttgacagatggtc-atgttgtttacagtga-ggttattattctgattttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA
|| | | | | ||| ||| || ||| || || ||| ||| || || | | ||| | | | | ||| |||||||| ||| | |||||||||||||| |||||||||||||| |||||||| || |||||||| |||||||||||||| ||||||
----gttttccctctctcacattcactgat---tatgatttggttcacggattgtctattttatatgggctgacaatgaccaacttacatttttagATTGCACCTATCATACATGAATGGACCTATGATGCCATGTGCCATGATTTACTAAATATGGAAGGAAATAAATATGTCCATGAA
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ13784 (Selaginella moellendorffii), 3'ss of exon 9
gtttcttagctccatttgttggtcattgacatgtaatattcttttgacagatggtcatgttgtttacagtgaggttattattctgattttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA
| | || || | | |||| | | || | |||||||||| |||||||| || ||||| || || ||||||||||||||||| | | | ||||||| | || ||| | ||
-------------------------------------gtaagtatggtgcttgtcagttctacctaca---aacctgacgtttgaag--cacagATTGCTCCCGTGATACACGAGTGGACATACGAGGCCATGTGTCATGATTTATTAAGTCTGGAGGGGAGCAAGTATACATACGAG
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ29221 (Selaginella moellendorffii), 3'ss of exon 9
gtttcttagctccatttgttggtcattgacatgtaatattcttttgacagatggtcatgttgtttacagtgaggttattattctgattttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA--------------
| | || || | | |||| | | || | |||||||||| |||||||| || ||||| || || ||||||||||||||||| | | | ||||||| | || ||| | ||
-------------------------------------gtaagtatggtgcttgtcagttctacctaca---aacctgacgtttgaag--cacagATTGCTCCCGTGATACACGAGTGGACATACGAGGCCATGTGTCATGATTTATTAAGTCTGGAGGGGAGCAAGTATACATACGAGGTAGATGTACCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttgacagatggtcatgttgtttacagtgaggttattattctgattttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA
ttctgat putative branch site (score: 3)
ttattattctgatttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcttagctccatttgttggtcattgacatgtaatattcttttgacagatggtcatgttgtttacagtgaggttattattctgattttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG